Multilocus profiling with AFLP, ISSR, and SAMPL.

Molecular markers which sample multiple loci simultaneously, like amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSR), and selective amplification of microsatellite polymorphic loci (SAMPL), produce highly informative fingerprints due to their high effective multiplex ratio and expected heterozygosity. Moreover, these markers can be generated for DNA of any organism without initial investment in primer/probe development or in sequence analyses. The fragments produced can be visualized either by agarose or polyacrylamide gel electrophoresis followed by autoradiography or silver staining or via separation and detection on automatic DNA sequencers. Here, we describe detailed protocols based on the original methods aimed to obtain these markers optimized to be resolved on polyacrylamide gel electrophoresis and detected by silver staining which provides a fast, sensitive, and cost-effective method.